I've posted to this thread before with the same problem, and the best suggestion I got was to try and bend the front of the bracket down just enough to snug in the front. I'm actually going to re-install my racks on my 'new' '08 this weekend and will give that a try. I tried in vain to try and get new yellow attachement pins, but the dealership can't even find them.

I agree that the design is weak. An adjustment screw to tighten would have been easy and made sense. Weak Toyota design doesn't happen often, but when it does its a head scratcher.

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im having my co worker ask some guys he knows at toyota about the issue ill let you know. but that yellow clip looks the same as a door panel clip i would try and use that as long as the prong is big enough for the hole to fit snug it will work..

The weather strip is cliped on by two clips on each side, the strips pop right off with minimal force.

here are the clips that hold the weather strip. ↓

Once removed, you will see three spots with a thick tape covering the threaded mounting holes. Remove the tape to uncover the holes. There are 5 treaded holes for the bolts per side. Two near the front, one in the middle, two near the back.

The first item bolted on is the front bracket. It uses the front two holes on the roof. All the bolts are either 25 or 30 torx heads.

Next, you will mount the one side of the rack.
The rack bolts up to the base with two bolts. Then also bolts up to the remaining 3 bolts on the rack to the roof.

Repeat on the pasenger side and the finished product should look like this ↓

and like this with the racks open ↓

In summary, theres only 14 bolts in total. The weather strips clip back on fairly easily if you decide to go back to stock. I believe there's a 100 lbs. limit for the OEM roof rack.

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On the front brackets, do you tighten them until the mastic(rubber) washers are flattened?

I just got mine installed yesterday and think I managed to avoid the "gap of woe".
My passenger side went right on with no problems.

I could not initially get my driver's side to engage the yellow clip into the bracket.
The problem appeared to be the ditch molding clip getting in the way.

The directions clearly state to pop the vertical walls off this sucker, but I did not have to do that on the passenger side.
Deciding that maybe those directions were there for a reason, I decided to try that. However, mine did not just pop off by whacking them with a trim tool as stated in the instructions. I had to use an X-Acto knife.

Voilà! The driver's side yellow clip engaged as easily as the passenger side.

Some additional information that may prove useful....
1.) My yellow clips were pre-installed in the tracks themselves, not in the bracket as shown in the OP's pics.

2.) I torqued everything down to the specifications provided in the directions. I used an el-cheapo torque wrench from Harbor Freight.
The specifications are as follows.

Bracket screws (2 each, pink thread lock): 117.7 lbf-in (13.3 N-m for our Canadian brethren)
Also, as stated in the directions I let them sit for 5 minutes and re-torqued.
The mastic washers clearly "squished" out at this torque.

Front Rail screws (2 each, blue thread lock): 50 lbf-in (5.6 N-m)

Long rail screws (3 each, green thread lock):117.7 lbf-in (13.3 N-m)

Overall, I'm happy with the install. I have more pics if needed, but the OP did a great job in the original write-up. I'm just trying to add some additional detail.

I stayed out in the freezing cold to install this tonight and well.. drivers side went on fine. the passengers side did not come with the rail attached. The long bolt they provided has nothing to screw into. Someone mentioned a tab of some sort that can fall out. is this tab on the bracket? Does anyone have a picture of this? I have looked everywhere and cant find any extra parts...

If it is what I am thinking of, it's a square metal plate (maybe 1/2" by 1/2") with a hole in it. The plate should be inserted into a square hole underneath where the long screw goes in. The plate can fall out when you start to mount the rail (this happened to me) but it sounds like you didn't even get that far. Not sure if I can find a picture.

Couple more things. The small plate is part of the rack. You would see it by flipping over the rack. Also, FYI, per the instructions the passenger side is supposed to come with the rail unattached. This is all by memory, so hopefully it's accurate.

Couple more things. The small plate is part of the rack. You would see it by flipping over the rack. Also, FYI, per the instructions the passenger side is supposed to come with the rail unattached. This is all by memory, so hopefully it's accurate.

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Yes the rail was unattached. I can see in the screw hole and there is a clip shape that could hold some sort of a plate.. maybe it fell out in the bed of the truck. I am not sure.. will have to look in the morning.

picked up a used rack and am wndering what to do about the mastic washers as i have none and cant seem to find any place that knows what they are let alone sells them. any ideas? i was considering maybe plumbers putty??

picked up a used rack and am wndering what to do about the mastic washers as i have none and cant seem to find any place that knows what they are let alone sells them. any ideas? i was considering maybe plumbers putty??

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I just installed a used roof rack last week. I used clear, all weather silicone. It's worked good so far. Roofer's tape would work good too, I've never used plumber's putty, but it sounds like it would do the trick.

I just installed a used roof rack last week. I used clear, all weather silicone. It's worked good so far. Roofer's tape would work good too, I've never used plumber's putty, but it sounds like it would do the trick.

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clear silicone huh? im sure ive got some clear silicone for windows and doors around. prob gonna have to try that... is that the all weather stuff like you are talking about? thanks for the info too!

Yeah that should work. Check the packaging, it should have a temp range and make sure it matches the climate you live in.

I'd suggest silicone-ing around the front holes and install the front metal bracket. Then test fit the rack on your roof, take it off, make any adjustments, add the silicone around the remaining bolt holes and then install the rack. If you squirt the silicone before you test fit, you can get silicone everywhere. I had to take the rack off and bend the metal brackets a little bit (they must've got bent up a little while they were off the truck).